Establishing a training set through the visual analysis of crystallization trials. Part II: crystal examples

As part of a training set for automated image analysis, crystallization screening experiments for 269 different macromolecules were visually analyzed and a set of crystal images extracted. Outcomes and trends are analyzed

Osservazioni

di Calogero Piro. Convertire la realtà che ci circonda in immagini, è stata fin dai primordi dell’essere umano un’atavica necessità. Ancora oggi nella nostra cultura visiva è tutto basato sull’utilizzo dell’immagine per conoscere la realtà che ci circonda. Con la scoperta della fotografia, la riflessione intorno alla natura si fa sempre più interessante. Il ruolo della macchina fotografica in questo progetto per raccontare l’ambiente, la struttura, gli oggetti, i segni, i colori e le atmosfere che caratterizzano il centro del CNR di capo Granitola ha trovato prepotentemente in questi giovani allievi della cattedra di fotografia dell’Accademia di Belle Arti di Palermo, diretta dal Professore Sandro Scalia, momenti di grande professionalità, realizzando un grande reportage con tutti gli aspetti essenziali della struttura e delle articolazioni primarie del linguaggio fotografico. Questa esperienza extradidattica difficile ed impegnativa non soltanto per la necessità del confronto col “nuovo” in termini organizzativi, ma anche per la necessità di descrivere attraverso la fotografia il tema della Biodiversità, è stato affrontato brillantemente. Mettendo in primo piano, siti naturali, siti storici come: Mozia e Selinunte, i laboratori del centro di ricerche, la Flora e la Fauna, sono riusciti a raggiungere con acuta osservazione ottimi risultati visibili in questo catalogo, e con la tangibile riprova di cosa possa e debba essere una educazione estetica assolutamente “libera” da condizionamenti, viatico ineludibile perché l’espressione artistica, sotto qualunque forma, sia artefice dei grandi processi di vera maturazione culturale, si avverte in questi giovani artisti la purezza e la consapevolezza dei propri messaggi ancora privi, e speriamo sempre, di qualunque tipo di inquinamento tendenzioso

Colorectal Cancer Stage at Diagnosis Before vs During the COVID-19 Pandemic in Italy

IMPORTANCE Delays in screening programs and the reluctance of patients to seek medical attention because of the outbreak of SARS-CoV-2 could be associated with the risk of more advanced colorectal cancers at diagnosis. OBJECTIVE To evaluate whether the SARS-CoV-2 pandemic was associated with more advanced oncologic stage and change in clinical presentation for patients with colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS This retrospective, multicenter cohort study included all 17 938 adult patients who underwent surgery for colorectal cancer from March 1, 2020, to December 31, 2021 (pandemic period), and from January 1, 2018, to February 29, 2020 (prepandemic period), in 81 participating centers in Italy, including tertiary centers and community hospitals. Follow-up was 30 days from surgery. EXPOSURES Any type of surgical procedure for colorectal cancer, including explorative surgery, palliative procedures, and atypical or segmental resections. MAIN OUTCOMES AND MEASURES The primary outcome was advanced stage of colorectal cancer at diagnosis. Secondary outcomes were distant metastasis, T4 stage, aggressive biology (defined as cancer with at least 1 of the following characteristics: signet ring cells, mucinous tumor, budding, lymphovascular invasion, perineural invasion, and lymphangitis), stenotic lesion, emergency surgery, and palliative surgery. The independent association between the pandemic period and the outcomes was assessed using multivariate random-effects logistic regression, with hospital as the cluster variable. RESULTS A total of 17 938 patients (10 007 men [55.8%]; mean [SD] age, 70.6 [12.2] years) underwent surgery for colorectal cancer: 7796 (43.5%) during the pandemic period and 10 142 (56.5%) during the prepandemic period. Logistic regression indicated that the pandemic period was significantly associated with an increased rate of advanced-stage colorectal cancer (odds ratio [OR], 1.07; 95%CI, 1.01-1.13; P = .03), aggressive biology (OR, 1.32; 95%CI, 1.15-1.53; P < .001), and stenotic lesions (OR, 1.15; 95%CI, 1.01-1.31; P = .03). CONCLUSIONS AND RELEVANCE This cohort study suggests a significant association between the SARS-CoV-2 pandemic and the risk of a more advanced oncologic stage at diagnosis among patients undergoing surgery for colorectal cancer and might indicate a potential reduction of survival for these patients

The detection and subsequent volume optimization of biological nanocrystals

Identifying and then optimizing initial crystallization conditions is a prerequisite for macromolecular structure determination by crystallography. Improved technologies enable data collection on crystals that are difficult if not impossible to detect using visible imaging. The application of second-order nonlinear imaging of chiral crystals and ultraviolet two-photon excited fluorescence detection is shown to be applicable in a high-throughput manner to rapidly verify the presence of nanocrystals in crystallization screening conditions. It is noted that the nanocrystals are rarely seen without also producing microcrystals from other chemical conditions. A crystal volume optimization method is described and associated with a phase diagram for crystallization

The structure of Plasmodium vivax phosphatidylethanolamine-binding protein suggests a functional motif containing a left-handed helix

The crystal structure of a phosphatidylethanolamine-binding protein from P. vivax, a homolog of Raf-kinase inhibitor protein (RKIP), has been solved to a resolution of 1.3 Å. The inferred interaction surface near the anion-binding site is found to include a distinctive left-handed α-helix

Structure of a Trypanosoma brucei α/β-hydrolase fold protein with unknown function

T. brucei gene Tb10.6k15.0140 codes for an α/β-hydrolase fold protein of unknown function. The 2.2 Å crystal structure shows that members of this sequence family retain a conserved Ser residue at the expected site of a catalytic nucleophile, but that trypanosomatid sequences lack structural homologs for the other expected residues of the catalytic triad

Efficient optimization of crystallization conditions by manipulation of drop volume ratio and temperature

An efficient optimization method for the crystallization of biological macromolecules has been developed and tested. This builds on a successful high-throughput technique for the determination of initial crystallization conditions. The optimization method takes an initial condition identified through screening and then varies the concentration of the macromolecule, precipitant, and the growth temperature in a systematic manner. The amount of sample and number of steps is minimized and no biochemical reformulation is required. In the current application a robotic liquid handling system enables high-throughput use, but the technique can easily be adapted in a nonautomated setting. This method has been applied successfully for the rapid optimization of crystallization conditions in nine representative cases